Table 1.

Improvement in TF role prediction using comparative genomics

	Escherichia coli K12			Saccharomyces cerevisiae			Homo sapiens
	Single	Multiple	Increase	Single	Multiple	Increase	Single	Multiple	Increase
	species	species	(%)	species	species	(%)	species	species	(%)
Significant TF–GO term pairs	0	14	NA	420	733	75	371	1112	200
GO terms per TF tested	0	0.16	NA	3.4	5.9	75	6.6	19.8	200
Covered TFs	0	9	NA	99	113	14	48	56	17
Term specificity	0	4.0	NA	4.5	4.6	2	3.8	4.2	11
TFs tested	85			124			56

The table shows FDR (q≤0.05) results for single- and multiple-species Gomo. The results shown are the total number of most-specific significant pairs (‘significant TF–GO term pairs’), the average number of most-specific GO terms per TF tested (‘GO terms per TF tested’), the number of TFs with at least one significant TF–GO term pair (‘covered TFs’), the average depth in the GO hierarchy of significant GO terms (‘term specificity’), and the total number of TFs in each experiment (‘TFs tested’). All results are for GC-compensated Ama scores and ‘full’ promoters of 500, 750 and 1000 bp for enterobacter, yeast and mammals, respectively. NA, not applicable.